The T-3000's sole mission is to protect and ensure the ultimate survival of Skynet, which seeks to eliminate the human race with its global machine network. The T-3000 describes itself as neither machine nor human; rather, it is a hybrid nanotechnological cyborg.[5] Producer David Ellison explains that the title Terminator Genisys "[is] in reference to genesis, which is in reference to the singularity and the man-machine hybrid that John Connor ends up being."[6]

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In a desperate effort to ensure its survival, the rogue artificial intelligence Skynet creates an avatar for itself in the form of a T-5000 (Matt Smith).[7] This Terminator travels through many timelines searching for a way to defeat the Human Resistance and ultimately infiltrates it under the guise of a fighter named Alex.[8] "Alex" is present as a soldier when John Connor and Kyle Reese (Jai Courtney) discover Skynet's time machine at the end of the war with the machines. As Kyle is being sent back in time to protect John's mother Sarah Connor (Emilia Clarke) from the T-800 Terminator sent to kill her in 1984, "Alex" carries out his attack. He kills all of the other soldiers nearby and infects John Connor with nanomachines, transforming him into a new hybrid Terminator designated as the T-3000. John Connor's conversion into a Terminator as Kyle travels back in time turns out to be such a major event that it leads to a fracturing of the timeline, completely rewriting the past and the future.[9][10]

The T-3000 is sent back in time to 2014, and given the mission to assist Cyberdyne Systems as the company's architect in developing a new operating system named Genisys, in addition to revolutionary robotic and time traveling technology, which is in reality Skynet and the recreation of its machines. When Sarah and Kyle arrive in 2017, he meets them at a hospital and convinces them that he really is John Connor, but his disguise is exposed by the Guardian (a reprogrammed T-800 portrayed by Schwarzenegger). The T-3000 engages the trio in multiple destructive battles before finally being destroyed by the Guardian by having his body disintegrated by a prototype time machine's magnetic field. Before his demise, the T-3000 furiously throws what remains of the Guardian's endoskeleton into a vat of mimetic polyalloy, inadvertently converting the Guardian into a nano-android with abilities similar to those of the T-1000, and saving the Guardian's life.

The Guardian explains during the film that before the final battle between Skynet and the Resistance, the former attempted to create a number of T-3000s, but the human subjects went insane and died; John Connor was the only known subject to survive the transformation reasonably mentally intact, albeit now loyal to Skynet as opposed to his previous loyalty to humanity.

The on-screen representation of the T-3000 was made by British effects company Double Negative. Footage would combine Jason Clarke filmed on set, keyframed animation, and motion capture. Supervisor Peter Bebb said that the company tried to design the T-3000 like a computer would do it, focusing on design and battle efficiency, "form follows function". Given it is a Terminator built out of a human, the result is "a pure robot that sits under flesh structure", still retaining an overall human shape. The mechanical cells tried to resemble the material on stealth aircraft, with a result described as "more matte than metal", resembling a slightly iridescentceramic carbon.[11][12]

The Guardian identifies the T-3000 with John's form and memories as being made of machine-phase matter (essentially, programmable matter) held together by a magnetic field.[13][14] Because of this, the T-3000's abilities far exceed those of the T-1000 and other Terminator models. It is capable of shapeshifting at much more rapid speed than the mimetic polyalloy Terminators, though it is still limited by complexity or mass; its transformation abilities are such that it can dissolve into its most basic form while falling head-first through the air, reorient itself to land on its feet and be fully transformed back to normal by the time it stands up. Likewise, it is capable of regenerating from almost any injury in mere moments. Unlike previous Terminators, the T-3000 transforms and regenerates in layers, beginning with its bone structure, then muscle tissue, skin and clothing. These layers can be adjusted independently of each other, as shown when John Connor adds and removes his facial scar at will in the film. These aspects, combined with the access the cyborg has to its original human host's memories in addition retaining his or her personality, behavioral traits, and some levels of emotions, the T-3000 can easily convince even those well-versed in tactics used by Terminators that it is actually a human, essentially a machine that thinks like them (see Turing test). This makes it more effective than other Terminators at infiltration. It appears to retain the ability to infect others and create more T-3000s, as it offers this to Sarah Connor and Kyle Reese in Terminator Genisys. The transformation, which is described as replacing its victim's body on the cellular level, cannot be reversed.

Though a formidable enemy, the T-3000 is not invulnerable. Because its abilities are primarily tied to its magnetic field, it is susceptible to magnetic attacks that disrupt said field.[15] Weaker magnetism is capable of disrupting or disabling the T-3000's shapeshifting and regeneration abilities, due to affecting its ability to manipulate its particles. A sufficiently strong magnetic field can pull the T-3000 apart briefly to restrain it, and, if its body is exposed to a powerful magnetic field for a sustained amount of time, the cyborg can be torn apart and terminated. The machine-phase matter is also vulnerable to the laser used in shaping mimetic polyalloy for use in the construction of T-1000s. If struck by this laser, the T-3000 can suffer enough external damage to render its outermost layer irreparably compromised, forcing it to discard its human appearance and use its true machine form. The T-3000 is still susceptible to some degrees of physical injuries and pains, and its agonies can escalate when it is under a magnetic attack. It is also shown to experience pain and have its movements impaired when trapped in an electrical current. However, these effects are only temporary due to its regeneration capabilities, which heal it once it manages to escape the current.